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- PDB-1ddm: SOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE -

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Basic information

Entry
Database: PDB / ID: 1ddm
TitleSOLUTION STRUCTURE OF THE NUMB PTB DOMAIN COMPLEXED TO A NAK PEPTIDE
Components
  • NUMB ASSOCIATE KINASE
  • NUMB PROTEIN
KeywordsSIGNALING PROTEIN/TRANSFERASE / COMPLEX / SIGNAL TRANSDUCTION / PHOSPHOTYROSINE BINDING DOMAIN (PTB) / ASYMMETRIC CELL DIVISION / SIGNALING PROTEIN-TRANSFERASE COMPLEX
Function / homology
Function and homology information


pericardial nephrocyte differentiation / Malpighian tubule tip cell differentiation / enteroendocrine cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation ...pericardial nephrocyte differentiation / Malpighian tubule tip cell differentiation / enteroendocrine cell differentiation / regulation of nervous system development / sensory organ precursor cell fate determination / sensory organ precursor cell division / neuroblast development / muscle cell fate specification / regulation of asymmetric cell division / regulation of neuroblast proliferation / glial cell migration / asymmetric neuroblast division / negative regulation of receptor recycling / basal part of cell / embryonic heart tube development / Notch binding / centrosome localization / negative regulation of neuroblast proliferation / positive regulation of endocytosis / negative regulation of Notch signaling pathway / neuroblast proliferation / regulation of neurogenesis / intracellular protein localization / cell cortex / negative regulation of gene expression / ATP binding / nucleus / cytoplasm
Similarity search - Function
NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily ...NUMB domain / Numb/numb-like / NUMB domain / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) / PH-domain like / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS
AuthorsZwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D.
Citation
Journal: EMBO J. / Year: 2000
Title: Multiple modes of peptide recognition by the PTB domain of the cell fate determinant Numb.
Authors: Zwahlen, C. / Li, S.C. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D.
#1: Journal: Nat.Struct.Biol. / Year: 1998
Title: Structure of a Numb PTB Domain-Peptide Complex Suggests a Basis for Diverse Binding Specificity
Authors: Li, S.C. / Zwahlen, C. / Vincent, S.J. / McGlade, C.J. / Kay, L.E. / Pawson, T. / Forman-Kay, J.D.
History
DepositionNov 11, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 10, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation
Category: database_2 / pdbx_nmr_exptl_sample_conditions ...database_2 / pdbx_nmr_exptl_sample_conditions / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_exptl_sample_conditions.pressure_units / _pdbx_nmr_software.name
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUMB PROTEIN
B: NUMB ASSOCIATE KINASE


Theoretical massNumber of molelcules
Total (without water)16,5552
Polymers16,5552
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 150STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
RepresentativeModel #1lowest energy

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Components

#1: Protein NUMB PROTEIN


Mass: 15277.424 Da / Num. of mol.: 1 / Fragment: PHOSPHOTYROSINE BINDING DOMAIN (PTB)
Source method: isolated from a genetically manipulated source
Details: CELL FATE DETERMINANT PROTEIN / Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Plasmid: PGEX4T2 / Production host: Escherichia coli (E. coli) / References: UniProt: P16554
#2: Protein/peptide NUMB ASSOCIATE KINASE / NAK


Mass: 1277.359 Da / Num. of mol.: 1 / Fragment: C-TERMINAL NAK 1437-1447 / Source method: isolated from a natural source / Source: (natural) Drosophila melanogaster (fruit fly) / References: EC: 2.7.1.37

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-SEPARATED NOESY
1222D 13C-HSQC
1333D 15N/13C-SEPARATED NOESY
143HNCO/CBCACONNH/HAHBCBCACONNH/HN(CA)CB/CCCTOCSYCONNH/HCCTOCSYCONNH/HCCHTOCSY/HALF- FILTER-NOESY
1542D TOCSY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY.

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Sample preparation

Details
Solution-IDContents
11MM PTB U-15N; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA
21MM PTB U-15N, 10% 13C; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA
31MM PTB U-15N, U-13C; 1MM NAK NA; 50MM PHOSPHATE BUFFER NA
41MM PTB NA; 1MM NAK (G1 F2 F7 F10) 15N, 13C;; 50MM PHOSPHATE BUFFER NA
Sample conditionsIonic strength: 50mM / pH: 6 / Pressure: 1 atm / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian UNITYPLUSVarianUNITYPLUS5001
Varian UNITYPLUSVarianUNITYPLUS6002

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Processing

NMR software
NameVersionDeveloperClassification
VNMR4VARIAN INC.collection
NMRPipe1.7F. DELAGLIOprocessing
NMRView3.1B. A. JOHNSONdata analysis
CNS0.3BRUNGERrefinement
CNS0.3BRUNGERstructure solution
RefinementMethod: TORSION ANGLE DYNAMICS USING ARIA PROTOCOLS FOR AMBIGUOUS RESTRAINTS
Software ordinal: 1
Details: THE STRUCTURES ARE BASED ON A TOTAL OF 2088 NOE, 50 DISTANCE RETRAINTS FORM HYDROGEN BONDS, 94 CHEMICAL SHIFT-DERIVED DIHEDRAL RESTRAINTS
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: STRUCTURES WITH THE LEAST RESTRAINT VIOLATIONS,STRUCTURES WITH THE LOWEST ENERGY
Conformers calculated total number: 150 / Conformers submitted total number: 20

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